Chapter 11 Skin microbiota: functional analysis
11.1 MCI
GIFTs_functions_community %>%
rowMeans() %>%
as_tibble(., rownames = "sample") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
# filter(time_point=="0_Wild") %>%
group_by(environment) %>%
summarise(MCI = mean(value), sd = sd(value))# A tibble: 2 × 3
environment MCI sd
<fct> <dbl> <dbl>
1 low 0.358 0.0521
2 high 0.295 0.0599MCI <- GIFTs_functions_community %>%
rowMeans() %>%
as_tibble(., rownames = "sample") %>%
left_join(sample_metadata, by = join_by(sample == sample))
# %>%
# filter(diet!="Post_grass")
shapiro.test(MCI$value)
Shapiro-Wilk normality test
data: MCI$value
W = 0.92978, p-value = 0.04846
Wilcoxon rank sum exact test
data: value by environment
W = 181, p-value = 0.001367
alternative hypothesis: true location shift is not equal to 0Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999
adonis2(formula = GIFTs_functions_community_dist ~ environment, data = sample_metadata %>% filter(sample %in% labels(GIFTs_functions_community_dist)) %>% arrange(match(sample, labels(GIFTs_functions_community_dist))), permutations = 999, by = "terms")
Df SumOfSqs R2 F Pr(>F)
environment 1 0.7443 0.19325 6.7072 0.003 **
Residual 28 3.1071 0.80675
Total 29 3.8514 1.00000
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.2 Wilcoxon
11.2.1 Community elements differences:
Elements low high Function
1 B0205 0.656049000 0.475561400 Amino acid biosynthesis_Threonine
2 B0207 0.558104900 0.437034800 Amino acid biosynthesis_Methionine
3 B0208 0.720234000 0.453394600 Amino acid biosynthesis_Valine
4 B0209 0.817868200 0.533705800 Amino acid biosynthesis_Isoleucine
5 B0210 0.743591700 0.450369200 Amino acid biosynthesis_Leucine
6 B0211 0.692446900 0.527403300 Amino acid biosynthesis_Lysine
7 B0212 0.662103100 0.482202700 Amino acid biosynthesis_Arginine
8 B0213 0.658973300 0.404776500 Amino acid biosynthesis_Proline
9 B0214 0.538837000 0.427169000 Amino acid biosynthesis_Glutamate
10 B0215 0.555625900 0.384205800 Amino acid biosynthesis_Histidine
11 B0216 0.656080300 0.398413900 Amino acid biosynthesis_Tryptophan
12 B0218 0.547111400 0.454774400 Amino acid biosynthesis_Tyrosine
13 B0219 0.130706150 0.053109630 Amino acid biosynthesis_GABA
14 B0220 0.278230900 0.157103900 Amino acid biosynthesis_Beta-alanine
15 B0221 0.611932300 0.441615300 Amino acid biosynthesis_Ornithine
16 B0303 0.262207900 0.219991800 Amino acid derivative biosynthesis_Ectoine
17 B0307 0.331732800 0.190395900 Amino acid derivative biosynthesis_Spermidine
18 B0309 0.163550590 0.066682630 Amino acid derivative biosynthesis_Putrescine
19 B0310 0.324450620 0.096901480 Amino acid derivative biosynthesis_Tryptamine
20 B0601 0.624014300 0.519070800 Organic anion biosynthesis_Succinate
21 B0602 0.822709900 0.702780300 Organic anion biosynthesis_Fumarate
22 B0604 0.442414500 0.663182100 Organic anion biosynthesis_L-lactate
23 B0605 0.345982500 0.192877900 Organic anion biosynthesis_D-lactate
24 B0701 0.634894500 0.480184300 Vitamin biosynthesis_Thiamine (B1)
25 B0702 0.816474800 0.727775100 Vitamin biosynthesis_Riboflavin (B2)
26 B0704 0.695651400 0.423724000 Vitamin biosynthesis_Pantothenate (B5)
27 B0705 0.427025500 0.322247500 Vitamin biosynthesis_Pyridoxal-P (B6)
28 B0707 0.761055800 0.687081300 Vitamin biosynthesis_Tetrahydrofolate (B9)
29 B0708 0.529524200 0.397595900 Vitamin biosynthesis_Cobalamin (B12)
30 B0802 0.834491600 0.525997700 Aromatic compound biosynthesis_Gallate
31 B0803 0.747515200 0.466065500 Aromatic compound biosynthesis_Chorismate
32 B0804 0.713239900 0.564040300 Aromatic compound biosynthesis_Dipicolinate
33 B1029 0.020309560 0.109015400 Antibiotic biosynthesis_Pyrrolnitrin
34 D0101 0.456920700 0.195072900 Lipid degradation_Triglyceride
35 D0204 0.380570100 0.297753100 Polysaccharide degradation_Chitin
36 D0206 0.330051000 0.188121700 Polysaccharide degradation_Alpha galactan
37 D0212 0.347270600 0.568537200 Polysaccharide degradation_Arabinan
38 D0213 0.183368100 0.104352100 Polysaccharide degradation_Mucin
39 D0308 0.195833000 0.100759700 Sugar degradation_L-Rhamnose
40 D0309 0.318345100 0.222315900 Sugar degradation_Galactose
41 D0310 0.022423170 0.195423010 Sugar degradation_NeuAc
42 D0501 0.621591000 0.281872700 Amino acid degradation_Serine
43 D0505 0.406362500 0.268585000 Amino acid degradation_Valine
44 D0506 0.413331800 0.225587800 Amino acid degradation_Isoleucine
45 D0507 0.464046400 0.327584800 Amino acid degradation_Leucine
46 D0508 0.327950100 0.201021000 Amino acid degradation_Lysine
47 D0512 0.453178200 0.259483100 Amino acid degradation_Histidine
48 D0601 0.346266800 0.600710800 Nitrogen compound degradation_Nitrate
49 D0603 0.190956000 0.100831600 Nitrogen compound degradation_Urate
50 D0613 0.770957000 0.465556200 Nitrogen compound degradation_Taurine
51 D0704 0.599817900 0.391382100 Alcohol degradation_Glycerol
52 D0706 0.002325978 0.005227122 Alcohol degradation_Ethylene glycol
53 D0816 0.254836100 0.147730100 Xenobiotic degradation_Phenylacetate
54 D0907 0.430336700 0.250939200 Antibiotic degradation_Tetracycline
55 D0908 0.313546400 0.169073500 Antibiotic degradation_Macrolide
11.2.2 Community functions differences
Code_function low high Function
1 B02 0.60472030 0.45731280 Amino acid biosynthesis
2 B03 0.30395930 0.15951330 Amino acid derivative biosynthesis
3 B06 0.70733810 0.63489430 Organic anion biosynthesis
4 B07 0.49899850 0.41498730 Vitamin biosynthesis
5 B08 0.47988990 0.39738120 Aromatic compound biosynthesis
6 B10 0.07930675 0.11431308 Antibiotic biosynthesis
7 D01 0.49240620 0.39070900 Lipid degradation
8 D03 0.25054260 0.17263400 Sugar degradation
9 D05 0.37578760 0.31196260 Amino acid degradation
10 D07 0.37342050 0.27095720 Alcohol degradation
11 D09 0.17066803 0.09778859 Antibiotic degradation
